Steflova, P., Tokan, V., Vogel, I., Lexa, M., Macas, J., Novak, P., Hobza, R., Vyskot, B., Kejnovsky, E.
GENOME BIOLOGY AND EVOLUTION
5:
769-782,
2013
Keywords:
sex chromosomes, sorrel (Rumex acetosa), transposable elements, satellites
Abstract:
Rumex acetosa is a dioecious plant with the XY1Y2 sex chromosome system. Both Y chromosomes are heterochromatic and are
thought to be degenerated.We performed low-pass 454 sequencing and similarity-based clustering of male and female genomic
454 reads to identify and characterize major groups of R. acetosa repetitive DNA. We found that Copia and Gypsy retrotransposons
dominated, followed by DNA transposons and nonlong terminal repeat retrotransposons. CRM and Tat/Ogre retrotransposons
dominated the Gypsy superfamily, whereas Maximus/Sireviruses were most abundant among Copia retrotransposons. Only one
Gypsy subfamily had accumulated on Y1 and Y2 chromosomes,whereas many retrotransposons were ubiquitous on autosomes and
the X chromosome, but absent on Y1 and Y2 chromosomes, and otherswere depleted fromthe X chromosome. One group of CRM
Gypsywas specifically localized to centromeres.Wealso found thatmajority of previously described satellites (RAYSI, RAYSII, RAYSIII,
andRAE180) are accumulatedontheYchromosomeswherewe identifiedYchromosome-specific variant ofRAE180.Wediscovered
two novel satellites—RA160 satellite dominating on the X chromosome and RA690 localized mostly on the Y1 chromosome. The
expression pattern obtained from IlluminaRNAsequencing showedthat the expression of transposable elements is similar in leaves of
both sexes and that satellites are also expressed. Contrasting patterns of transposable elements (TEs) and satellite localization on sex
chromosomes in R. acetosa,where not only accumulation but also depletion of repetitiveDNAwas observed, suggest that a plethora
of evolutionary processes can shape sex chromosomes.
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IEB authors: Roman Hobza
Čeština
English